Clayton Forrester/Frank was the best combination of mad scientists, so I voted for Clayton. But Pearl eventually grew on me, and I really don't think she's that far behind. The "Public Pearl" segment where she sings "When Loving Lovers Love" with Brain Guy is one of my all-time favorite host segments.

"Clive [Barker]'s idea of a great time is to have a nightmare about a woman with three heads and no skin who flays your body with a pitchfork. To give you some idea, NIGHTBREED has over 200 pus monsters, including one guy with a crescent moonhead like the McDonald's commercial and a fat guy with snakes that pop out of his stomach and eat your face off, and these are the GOOD GUYS. These are the people we're supposed to LIKE."-Joe Bob on NIGHTBREED

It seems that I'll be in the minority here, and while Clayton may be the funnier of the two-I think you (or I, more accurately) could say that Pearl was a better character.

Before the jump to the Sci-Fi channel, all the MST3K episodes were essentially stand alone episodes, with no a whole lot of continuity between them, save for the occasional reoccurring character. Once on Sci-Fi channel, the host segments took on a more story based theme, with the show having arches that went one from one episode to the next. We got to see Pearl, Bobo and Brain Guy in different environments, situations, and such. Heck, Pearl even once voluntarily went into the theater to better understand what was going on. And while I might not use the term realistic character growth, it did seem that because they were now in different territory on occasion, Pearl got more experience out of the experiment, while Clayton never really left the lab. (and yes, I'm aware a lot of that had to do with the budget, and there's probably episodes to provide counter arguements).